Output from the Identify QIAseq Multimodal DNA Library Kit Variants workflows
The following outputs are generated:
- Genome Browser View (
): A collection of output tracks, allowing multiple data types at the same genomic position to be viewed simultaneously. Note that not all output tracks are necessarily in the browser. Tracks can be added and removed from the browser.
- Sample report (
): A report containing essential information from all reports produced by the workflow. See Create Sample Report output for details.
- Variants passing filters (
): The filtered variants.
- Gene-level CNV track (
), if running the Identify QIAseq Hybrid Capture DNA Somatic Variants (with UMI) (Illumina) workflow with CNV detection:
Genes affected by CNVs. See Gene-level annotation track for details.
- QC & Reports folder:
- Coverage report (
): Summarizes the coverage.
For the Identify QIAseq Multimodal DNA Library Kit with UMI Somatic Variants (WGS) (Illumina) workflow:
- Coverage is summarized across the entire genome. See QC for Read Mapping for details.
For the Identify QIAseq Hybrid Capture DNA Somatic Variants (with UMI) (Illumina) workflow:
- Coverage is summarized within the target regions. See Coverage summary report for details.
- Mapping report (): Summarizes the performed read mapping. See Summary mapping report for details.
- QC report (): Summarizes and visualizes various statistics of the input reads. See QC for Sequencing Reads for details.
- Remove and annotate UMI report (): Summarizes the identified UMIs. See Remove and Annotate with Unique Molecular Index for details.
- Remove ligation artifacts report (): Summarizes ligation artifacts found in and removed from the read mapping. See Remove Ligation Artifacts for details.
- Structural variants report (): Summarizes the number and different types of identified structural variants. See Output from the Structural Variant Caller for details.
- Trim reads report (): Summarizes the performed read trimming. See Trim output for details.
- UMI group report (): Summarizes the identified UMI groups. See Calculate Unique Molecular Index Groups for details.
- UMI reads report (): Summarizes the UMI reads. See Create UMI Reads from Grouped Reads for details.
Additionally, if running CNV detection, TMB score calculation, and MSI detection:
- CNV results report (): Summarizes the identified CNVs. See CNV results report for details.
- MSI report (): Summarizes the performed MSI detection and contains the MSI status of the sample. See Output from Detect MSI Status for details.
- TMB report (): Contains the TMB score and confidence values. See Calculate TMB Score for details.
- Coverage report (
- Tracks folder:
- Indels indirect evidence (): The filtered indels generated by the Structural Variant Caller. See Output from the Structural Variant Caller for details.
- Mapped UMI reads (
): The UMI reads mapped to the reference genome.
- Unfiltered variants (): The variants identified before filtering.
Additionally, for the Identify QIAseq Hybrid Capture DNA Somatic Variants (with UMI) (Illumina) workflow:
- Amino acid track (
): The amino acid changes introduced by variants in the filtered variant track. See Amino Acid Changes for details.
- MSI loci track (), if running MSI detection:
MSI loci annotated with predicted stability. See Output from Detect MSI Status for details.
- Per-region statistics track (): Coverage statistics for each target region. See Per-region statistics for details.
- Region-level CNV track (), if running CNV detection:
Regions affected by CNVs. See Region-level annotation track for details.
- TMB somatic variants (), if running TMB score calculation:
Filtered variants that are included in the TMB score calculation. See Calculate TMB Score for details.
- Target regions without XY (): Target regions that can be used for CNV detection, where regions on X and Y chromosomes are removed.
- Indels indirect evidence (